Contacts of the strand formed by residues 73 - 77 (chain C) in PDB entry 1VBF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 73 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLY 3.9 0.6 + - - +
72C GLN* 1.3 74.5 - - - +
74C VAL* 1.3 61.4 + - - +
93C ASP* 6.2 0.2 - - + -
94C LYS* 3.3 28.3 - - + +
96C VAL* 4.6 1.3 - - + -
132C GLU* 2.7 61.5 + - - +
134C PRO* 3.3 23.1 + - + +
135C TYR* 3.6 15.4 - - + -
136C ASP* 2.9 37.8 + - - +
137C ARG 3.6 2.6 + - - -
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 4.6 1.3 - - + -
68C LEU* 3.8 13.5 - - + -
72C GLN* 4.4 3.8 - - + -
73C LYS* 1.3 77.3 - - - +
75C LEU* 1.3 76.8 + - - +
76C GLU 4.5 0.2 - - - +
88C ILE* 4.0 23.3 - - + -
92C VAL* 3.4 31.9 - - + -
94C LYS 2.9 10.2 + - - +
95C VAL* 3.4 3.9 - - + +
96C VAL* 2.8 30.0 + - - +
135C TYR* 3.9 4.7 - - - -
137C ARG* 3.6 23.1 - - + +
139C VAL* 4.5 13.2 - - + -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 1.3 78.2 - - - +
76C GLU* 1.3 65.6 + - - +
77C ILE* 4.4 10.3 - - + -
96C VAL* 3.3 28.0 - - + +
98C VAL* 4.5 7.2 - - + -
128C GLY* 3.9 15.9 - - - -
129C TYR* 3.9 9.9 - - + +
135C TYR* 3.7 33.1 - - + +
137C ARG 3.1 5.7 + - - -
138C VAL* 3.2 24.2 - - + +
139C VAL 3.2 21.8 + - - -
151C PRO* 4.7 5.8 - - + -
154C GLN* 3.7 23.3 - - - +
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Residues in contact with GLU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL* 5.1 0.4 - - + -
75C LEU* 1.3 76.0 - - - +
77C ILE* 1.3 64.6 + - - +
78C GLY 3.8 10.3 - - - +
79C THR* 3.5 4.4 - - - +
84C TYR* 4.0 5.4 - - - +
85C THR* 2.5 37.8 + - - -
88C ILE* 4.3 13.7 - - + +
95C VAL* 4.7 7.9 - - + -
96C VAL 2.7 13.0 + - - +
97C SER* 2.4 31.8 + - - +
98C VAL* 2.8 27.9 + - - +
139C VAL* 3.7 6.7 - - + +
141C TRP* 3.0 33.0 + - + +
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Residues in contact with ILE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C LEU* 4.4 15.3 - - + -
76C GLU* 1.3 74.6 - - - +
78C GLY* 1.3 60.6 - - - +
98C VAL* 4.2 3.8 - - + +
125C GLY* 3.3 43.7 - - - +
128C GLY* 5.1 0.9 - - - -
138C VAL* 4.4 2.9 - - + -
139C VAL 2.9 14.6 + - - +
140C VAL* 3.6 19.6 - - + +
141C TRP* 3.1 27.5 + - - -
142C ALA* 5.9 0.3 - - - +
148C LEU* 4.5 3.1 - - + -
151C PRO* 3.3 32.3 - - + -
161C MSE 4.3 1.6 - - + -
196C ILE* 4.0 20.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il